[gmx-users] 4xRE: COM motion removal (further clarification)

Janne Hirvi janne.hirvi at joensuu.fi
Wed Jul 5 13:59:34 CEST 2006

> >In my case I need to see COM motion when my water droplet (starting from
> >spherical droplet) is spreading on a surface, but I used option 'comm_mode 
> >= none' and now I think that I should have used 'comm_mode = linear' with 
> >large nstcomm (earlier with small nstcomm I did observed anomalous behaviour

> >without clear spreading) so that I actually see that droplet spreads but I  
> >wont see large lateral motion of COM? Do you have a comment on that?
> Are you talking about the center of mass of the total system
> or the centers of mass of the surface and water?

My system consists of a large frozen surface and small water droplet (starting
from spherical droplet (180 degrees)). COM should change (z-dimension should
decrease) when droplet spreads on a surface and finds its "equilibrium contact
angle". Actually the center of mass of the droplet and the center of mass of
the system should change.

> The center of mass of the total system is a free degree of freedom.
> Since no forces are working on it, its momentum should not change.
> But do to integration errors it could. To avoid this annoying, though
> unharmful, behavior one should use comm_mode=linear, ntscomm=1.

To see this change in the z-coordinate of the COM I have to use comm_mode=none
or com_mode=linear with nstcomm>>1.

> You can not remove the separate com motion of the surface and
> the water as this would influence the process you want to study.

I would imagine this is a situation in bulk simulation but what is the situation
in my case (frozen surface+droplet)? I have tried to remove COM motion of the
droplet and the whole system and the final results are pretty equal (also equal
to calculation with comm_mode=none but without lateral motion on surface).
However when removing COM motion of water droplet I have to use much larger
nstcomm (>2000) to see as quick spreading as in case of comm_mode=none or
comm_mode=linear with nstcomm=100. 

> Berk.

Thanks again for helping me!!!


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

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